Secrets of the Mind
by MacGateFan
Summary: John and Elizabeth are captured. John is released and is allowed to return to Atlantis. But what about Elizabeth? And why is John Sheppard the only person she can remember? SheppardWeir.
1. Chapter 1

Title: Secrets of the Mind  
Rating: PG13  
Author: MacGateFan  
Disclaimers: All characters and concept belong to MGM Studios and other people who aren't me. The story idea is all mine, though.  
Note from the author: Thanks to the lovely, xfirefly9x, for taking the time to beta this fanfic.

* * *

John woke up to a pounding head and arm that were competing for attention. He glanced at his forearm to see gauze wrapped tightly around it. He immediately remembered the slice of a knife through his skin and why he had received it.

Elizabeth.

_She had come with him off world to check on one of Major Lorne's friendly allies. Everything had gone smoothly until they were getting ready to dial Atlantis. Suddenly they were surrounded by a group of crazily dressed natives, and one had Elizabeth in his grasp._

_John lunged for the one who held Elizabeth and a knifepoint. He knew it probably wasn't the smartest thing to do, but he didn't want her to get hurt. Not that he wanted to get hurt, but it happened anyway._

_"Stop!" Elizabeth let out a small cry as the force of a blow knocked her down._

_John looked over at her as they were now next to each other on the ground. He noticed a bruise forming on her cheek and didn't even think as he moved to attack again. The last thing he saw was Elizabeth's worried expression._

Now he was waking up alone in some foreign cell and Elizabeth was nowhere to be seen. John gingerly stood up, hand on the wall for support. He slowly moved towards the door to the cell and by the time he reached it, his head was pounding unmercifully.

He closed his eyes and took a deep breath. Elizabeth was counting on him to get her out of here... wherever she was. John stepped back when he heard a key in the lock. Looks like he was going to get his answers.

Elizabeth was thrown into the room with a cry. He was about to help her up when one of the guards grabbed him and pulled him towards the door. "You are free to go," he sneered.

"I'm not leaving without her!" John exclaimed, shoving Burly Guard #1. He was distracted long enough for Burly Guard #2 to grab his injured arm. "Elizabeth?"

He was a little worried when she didn't respond to him. Before John could say anything else, Burly Guard #1 pulled him out of the cell, slamming the door shut. "Stop! Why are you doing this? Let her go!"

Burly #1 yanked at his hair. "If you don't shut up, we will kill her now!"

John just glared at the guard and calmed himself. He would let it go for now, but he would be back to this planet with plenty of ammunition. He knew Carson wouldn't be happy, but that's how it was going to be.

About 20 minutes later, he was back at the 'Gate dialing Atlantis. He was a bit surprised his vest and transmitter were given to him. However, John Sheppard was not about to look a gift horse in the mouth.

John saw Rodney heading over to him once he stepped from the event horizon. The astrophysicist's words died on his lips when he saw his friend. "Get a medical team down here!" he exclaimed.

"I'm fine," John replied, taking a deep breath as a wave of dizziness washed over.

Rodney immediately grabbed his arm, being careful to avoid the injured one. "Quit being macho," Rodney said, helping him to the floor. "Where's Elizabeth?"

"They still have her." John attempted to stand up again just as Carson and his team arrived. "Get a team together, Rodney, we're going back!"

Carson could tell that John was fighting on pure adrenaline. He moved closer to his patient. "Colonel, don't worry about Dr. Weir. Rodney will get Teyla and Ronon and they'll bring her back, I promise."

"No!" John exclaimed as his knees buckled. Rodney and Carson barely caught him in time. "I have to go, I left her behind! They said if I didn't, they would kill her."

By this time, Carson's team had managed to get John onto a gurney. "Relax, son," Carson said, "everything will be all right."

John finally let the overwhelming darkness surround him.

* * *

Elizabeth stared at the woman in front of her in complete shock. Malott was accusing her of staring lustfully at her husband Raxton.

She remembered Raxton from her meeting with Saleena, President of the small country. As far as she could tell he was a very nice man. She had no thoughts about him other than that and she told Malott as much.

Malott circled Elizabeth like a hawk. There was so much hatred in the woman's eyes. "I am sorry about this," she told Malott. "I never meant for this to happen."

"Silence!" Malott growled.

"Where's Colonel Sheppard?"

Malott seemed to smirk at Elizabeth. "He is dead."

Elizabeth's heart leapt into her throat. "No! You're lying!" Malott tossed her something and she couldn't hold in the gasp that escaped her lips. It was a torn piece of John's shirt… and it was soaked in blood.

Suddenly, Malott grabbed her arm, squeezing tightly, and pulled her down the hall. "You will be punished for what you have done!"

Elizabeth was brought into a small room with a single chair in the middle. Malott practically threw her onto it. Elizabeth felt her arms being wrenched behind her and tied.

"This is a friend of mine," Malott was saying. "He is a physician and will be treating your symptoms."

She stared at Malott. "My symptoms? I assure you, I am perfectly healthy. The only thing that's wrong is that I'm sitting in this chair and not you."

Malott shrugged and Elizabeth watched in horror as the man moved towards with a syringe. It was filled with a bright green liquid. She could only imagine what was in there.

"In a few minutes, your mind and everything in it will be lost forever, Dr. Weir. When the serum has fully worked itself into your system, you will be free to return to your home. I promise."

"For some reason I don't really believe you," Elizabeth responded. Outside she was the picture of calm, but inside, Elizabeth had never been more nervous or scared in her life. She was about to lose every memory within her mind.

She felt her eyelids grow heavy and fought to keep them open. As she slowly gave in, her last thoughts were of John Sheppard and how she never got to say goodbye.


	2. Chapter 2

Secrets of the Mind  
Part 2  
Disclaimers in Part 1

* * *

Just as Rodney was about to have Chuck dial the 'Gate, the alarm for an incoming wormhole sounded. He glanced over at him patiently, hoping for Elizabeth's IDC. Chuck shook his head. "Just a transmission, Dr. McKay. They'd like to speak to Colonel Sheppard."

"I'll take it," Rodney replied. "This is Dr. Rodney McKay. Colonel Sheppard is unavailable right now. Who is this?"

"Dr. McKay, it is President Saleena. We have located the whereabouts of Dr. Weir. She has been taken by my advisor's spouse to be punished."

Chuck noticed Rodney visibly pale at that. "What the hell is she being punished for and why haven't you saved her yet?"

"Please calm down, Doctor," Saleena replied. "We have a team of soldiers heading there now, but I thought you should be informed."

Rodney took a deep breath. "I apologize, President Saleena. We'll be there shortly."

Once the wormhole shut down, everyone looked at Rodney in relief. "Chuck, get Teyla, Ronon, and Major Lorne's team up here."

Rodney was pacing back and forth in the conference room when everyone showed up. "Are we ready?" he asked as Teyla handed him a TAC vest.

"We are now."

"Carson?"

The Scotsman regarded his friend. "Colonel Sheppard is sleeping soundly and his fever has gone down. I thought you should have a medic with you and I volunteer myself."

"We should go," Ronon said.

When the team arrived on the planet, President Saleena greeted them with a bow. She presented the man next to her. "This is Raxton, he is Malott's husband. Malott is the one who captured Colonel Sheppard and Dr. Weir."

Ronon glared at the man, but Lorne held him back. "It's not his fault, big guy," he said.

Raxton stepped forward, ignoring Ronon and his death glare. "I must apologize for my wife's behavior. She is a very sensitive and jealous woman. After all these years, I thought she had grown out of it. I thought that she had learned to trust me, but I guess I have been mistaken."

"We do not blame you," Teyla said with a sad smile. "We only wish to find Dr. Weir and bring her home."

"Come!" Saleena said. "The soldiers should have returned by now. We will have one of our doctors see to her care."

Carson spoke up. "If it's all right, Love, I'm her doctor. I'll be the one to look after her."

Saleena nodded. "Very well."

Lorne noticed that Rodney was too quiet and stepped back to walk next to the astrophysicist. "You all right, Dr. McKay?" he asked.

"What? Huh? Oh yeah. Just thinking."

When it seemed that Rodney wasn't going to elaborate on his feelings, Lorne let it go. He understood when you just needed to sort things out on your own and there seemed to be a lot of sorting going on around here.

The team finally arrived to the consulate where Major Lorne had first negotiated with President Saleena and her Council. She led them inside and towards the medical wing. "Dr. Beckett, would you care to join me?"

The others were about to protest, but Saleena held up her hand. "I am sorry, but only physicians are allowed in the treating area."

"Don't worry," Carson said. "I'm sure she's all right. I won't be long and we can get back home."

Carson followed Saleena into them towards the one occupied bed in the room. A nurse was whispering quietly to the patient in the bed. Carson smiled when he saw her look up at him, but she seemed to shrink away.

Not thinking anything of it, Carson walked over and immediately took her hand. "Elizabeth, Love, are you feeling all right?"

She looked up at him in confusion. The man did not seem familiar to him at all. It was not the face of the one she longed to see. To hold. And why was he calling her Elizabeth? Was that her name?

"Who are you?" she finally asked.

"Excuse me?" Carson was shocked to say the least. That was not what he was expected to hear from her.

Elizabeth looked over at the nurse, who nodded reassuringly. "I'm sorry…"

"Carson."

"Carson. I don't remember who I am or where I come from. I take it you know me." At his nod, she continued. "Is Elizabeth my name?"

"Aye that it is."

"Where's John? They told me he was dead, is that true?"

Carson was the confused one now. How could she remember Colonel Sheppard, but nothing else? "Um, he's back home waiting for you, Elizabeth."

"So he's safe?" she inquired.

"Aye."

"I want to see him."

Carson nodded, helping her to stand as the nurse brought over a pair of shoes for her. She stopped a moment as a wave of dizziness washed over. "I'm all right," Elizabeth whispered.

"If you could wait here, I'd like to talk to you friends about your condition. I don't want them to bombard you with question upon question and I don't want you to feel uncomfortable because you don't remember them."

"I'd appreciate that."

Carson popped his back in the room a few minutes later. "We're ready to go, Love."

"Okay, I can do this!" Elizabeth said, taking a deep breath.

Rodney was pacing back and forth as Carson went back into the room to get Elizabeth. He couldn't believe what was happening. He was just happy that President Saleena gave them some of the serum the crazy man injected into her. Then at least Carson could do his voodoo magic and help her.

Elizabeth seemed weary as she joined them in the hall. No one said anything as Carson and Teyla thanked President Saleena. They promised to keep in touch regarding Elizabeth's progress, but they would have to evaluate the negotiations at a later date. The President seemed to understand this with much disappointment.

Elizabeth was highly agitated by the time they arrived in the infirmary. She insisted on seeing that John was alive and breathing before she allowed Carson to check her over.

He watched in concern as they arrived at John's side and Elizabeth took his hand. "Will he be all right?"

"Aye, Love. His arm was infected so he has a slight fever. It's not too serious. Why don't we go to the bed near the window? You have a view of the ocean and you can see Colonel Sheppard from here as well."

Elizabeth nodded. "Thank you… Carson," she said, looking at the floor. "I don't know why I remember his name and face so clearly, but I don't know who he is or who any of you are. I don't even know where I am!"

"I'm having tests run on the serum they injected you with, but if I hazard a guess, Colonel Sheppard was most likely the last person you were thinking of before the serum took effect."

"Maybe," she replied, uncertain.


	3. Chapter 3

Secrets of the Mind  
Part 3  
Disclaimers in Part 1

From the Author: Thank you so much for the reviews. I really appreciate it and I'm glad you're enjoying my fanfic. More to come!

* * *

John woke up feeling one hundred times better than before. He looked around the room, but didn't see Carson or any of his staff. Glancing to his right, he gasped. Elizabeth was sleeping soundly on one of the infirmary beds. 

He carefully removed the IV from his hand and swung his legs off the bed. The floor was freezing, but he didn't care. He had to be certain she was all right. A wave of dizziness caught him off guard, but he fought it and was at her side before he knew it.

"Elizabeth," he whispered, taking her hand.

She blinked her eyes open and smiled the minute she saw him. "Are you feeling all right?" she asked.

"I'm fine. What about you?" He asked, trailing the bruise on her cheek.

"I was just worried about you," Elizabeth replied. "Should you really be out of bed? Carson says you have a fever."

John ignored the comment. "Did they hurt you?" he asked. "The last time I saw you, they were throwing you into the cell and you didn't answer when I called your name."

"I…" Elizabeth realized then that John had no idea about the serum she was given. She could tell that he was feeling guilty about what happened to her. How could she tell him what happened when he felt that way?

"What's wrong? Elizabeth, I can tell from the expression on your face that something happened. Tell me."

Elizabeth took a deep breath. "Carson said they injected me with a serum that causes memory loss." She held up her hand when he was about to speak. "I don't know why I remember you. I mean I just remember your name, face, and that we have a connection. I don't really know who you are or where this place is."

John stared at her in disbelief. "I'm sorry," he whispered.

"Don't be sorry," she said, taking his hand. "You had nothing to do with this."

He merely nodded, the room becoming slightly tilted. John barely heard Elizabeth calling his name as his had begun to pound. Was it just him, or was it getting really hot in the room?

He felt lightheaded and as if he was floating across the floor towards his bed. John blinked a few times as someone helped him lie down. "Carson?"

"Aye, Colonel. You shouldn't have gotten out of bed."

"Sorry," he muttered. "I just had to make sure… I mean you weren't around to ask… Sorry." John was too exhausted so he gave up.

Carson patted his friend on the shoulder. "It's quite all right. I understand, after all you were worried about her. Now that you know she's safe, why don't you get some rest?"

Elizabeth watched the pair in silence. She had a feeling there was more to her relationship with John than he was telling her. Her heart felt light when he had walked over to her and began talking. He was adorably cute and she couldn't help but feel safe when he was around.

"Elizabeth."

She blinked and looked up. The woman who was with Carson on the planet stood before her. "Teyla, right?"

"That is correct," Teyla replied with a nod. "I just came to see how you were feeling. Carson states that you'll be released shortly and he has asked me to take you to your quarters to get you settled in."

Elizabeth smiled. "Thank you, Teyla. I would appreciate it." She paused in thought for a moment. "May I ask you something?"

"Of course."

"Is Colonel Sheppard involved with anyone?"

Teyla was confused. "Involved?"

"Is he married or..."

"Oh, no!" Teyla replied. "At least, he has not said so. I like to think I know Colonel Sheppard well, but even he has his secrets. Why do you ask?"

Elizabeth began ringing her hands in nervousness. "I think... I think I love him."

* * *

Rodney entered the infirmary and saw John tying his shoes. "I guess you're feeling better." 

"It would appear so," John replied, straightening. "I've been cooped up in here for nearly a week. Nothing against Carson, but I am so ready to get out of here."

"How's your arm?"

"A little sore, but nothing I can't handle."

Rodney scoffed. "You'd say that even if your entire arm had been removed."

John shook his head. "Whatever. Have you seen Elizabeth? Carson said the only time she's been in here is when I'm sleeping. It's like she doesn't want to talk to me or something."

"Last time I saw her, she was in the mess hall with Teyla. Her memories are still intermittent at best. Unfortunately Carson hasn't been able to find anything to counteract the serum."

"Yeah, that's what he said. What have you guys done to jog her memory?"

"Well, we were going to take her to Earth, but she was worried something would happen to you while we were gone with having to take the Daedalus back so we gave her mission reports to read instead."

John's eyes widened as they headed into the hall. "Please tell me you gave her the lighter reports to read. Somehow I think reading about attacks by the Wraith and Genii would only make it worse."

"Oh no," Rodney replied sarcastically. "The first one we gave her to read was you turning into a bug."

"Ha ha. And don't ever mention that again, Rodney!"

The pair arrived in the mess hall and after they grabbed trays of food (Rodney having enough to feed a small army); they headed over to where Elizabeth and Teyla sat. John noticed that Elizabeth looked a little sad.

"Hey," he said

The minute she saw him, her shoulders slumped even further. Elizabeth was not ready to deal with these feelings. Or maybe she was and that's why she was scared. "Um, excuse me," she gasped out, pulling herself to her feet. She purposely avoided John's eyes and hurried off.

John stared after her for a moment before following, leaving his tray behind on the table. "Elizabeth!"

Before Rodney or Teyla could say a word, they were both gone. "Maybe I should check on them," Rodney suggested after a few minutes.

"They will be fine, Rodney."

"You know something, don't you?"

Teyla shook her head, taking a sip of water. "I don't know what you mean."

"Teyla, please. You can't even look me in the eye."

"Very well, Rodney," she replied. "Elizabeth told me of her feelings for Colonel Sheppard. At least, what she thinks her feelings are for him. I don't know if they're true and were hidden deep in her mind for awhile or..."

Rodney was not a very patient man. "What feelings?"

"She said she loves him."

"Oh."

He sat there in silence as he contemplated what Teyla just told him. Elizabeth's thoughts had to be subconscious. Or maybe they weren't but she knew she couldn't act on them. Now with that serum she's lost and confused and who knows how John would take this or if he even felt the same.

* * *

"Elizabeth!" John called. "Elizabeth, wait!" 

He saw her turn the corner and head out to the balcony. He was silently happy about that because he was a little exhausted from their jog through the city. What had caused her to freak out like that?

John was about to speak up when suddenly Elizabeth turned around, pulled him towards her, and kissed him. John was shocked to say the least and yet he couldn't pull away.

He had wanted this for so long, but he knew it could never happen. Not while they worked together. John gently pulled away from her and they both stared, too stunned to say anything.

Elizabeth searched John's eyes for approval of what she had done, but all she saw was fear. He was scared. Of what? Her? "I'm sorry!" she cried, running back inside.

As John watched her leave, he saw Rodney standing there, mouth open. "Close your mouth, Rodney, you'll catch flies."

Rodney tried to get John to answer him as he followed his friend. He was about to give up when John swayed and nearly fell over. Rodney immediately rushed to his side.

"You're overdoing it, Sheppard. Carson is going to be so pissed."

"Rodney, I'm fine," John replied. "Just a little tired."

Rodney sighed. "Right and I'm not the smartest person in this city. Come on, if you won't see Carson then I'm taking you to your quarters and you're going to sleep."

John reluctantly went with Rodney as he continued to process what just happened. How long had Elizabeth felt that way and was that what she really felt? He just didn't know, but he was scared to find out.

He didn't know when he realized Elizabeth was more than just a friend. Right now it didn't matter. What mattered most was trying to sort out these feelings swimming within his mind.

John squeezed his eyes shut as his head began to pound. He would sort everything out later. Right now, he wanted some aspirin and a bed. He must have been way out of it because as Rodney was helping him lie down, he saw Carson heading over to them.

Damn, John thought, that sneak!

"Rodney?"

"Carson, he chased Elizabeth half way through the city and was exhausted," Rodney said. "When he tried to brush me off, he nearly collapsed."

Carson pursed his lips as he checked John's vitals. "Blood pressure is slightly elevated. And it looks like your fever's returned, Colonel."

"Sorry, Doc," he muttered sheepishly.

"You need to take better care of yourself," Rodney told him. Carson and John stared at him. "What? Do you really think I want to be in charge of Atlantis? I am perfectly happy sitting in my lab. I have no desire to order people around and do paperwork."

The two continued to stare at him. "Okay, I do like ordering people around."

* * *

Elizabeth soon found that she was lost in more ways than one. She had run away and even though it had seemed like a good idea at the time, Elizabeth was beginning to realize that she had no clue where she was. 

Who could she call? John was definitely out of the question. So was Carson. He'd be overly worried about her running around. Not Rodney. He was probably dealing with John right now. Elizabeth took a deep breath.

"Teyla?"

"Yes, Elizabeth?" The young woman's voice filtered through.

"This is probably going to sound stupid, but I'm… lost."

"Do you notice anything around you that may help me locate you?"

Elizabeth looked around. Everything looked the same. "I was originally on the East Pier and turned to the right. Does that help?"

"It does, Elizabeth," Teyla replied. "I will double check your location with Dr. Zelenka only."

"Thank you."

She was relieved that Teyla wasn't going to announce to the entire expedition that she had no clue where she was. Elizabeth took a seat against the wall and closed her eyes as she waited. She immediately opened them as memories of the kiss floated back to the surface.

It was a beautiful and passionate kiss, yet she could sense confusion and underlying fear in John. She wanted to know why and how she could help him, but she was just as scared. Were these feelings real? Would she ever remember who she was?

"Elizabeth." She almost didn't notice Teyla kneeling next to her. She took a deep breath and looked up at the Athosian. "Are you all right?"

She smiled. "I'm fine. I was just thinking. Trying to help my memories to return."

"Perhaps I can help you with that," Teyla suggested, helping her up.

"How?"

The pair walked down the hall. "My people believe that meditation is a good way to put ones life into perspective. We also find that it helps us to unlock memories we've had buried for so long."

"I'd like to try that. Thank you, Teyla."

"You are welcome."

* * *

John sat quietly in the infirmary bed. His fever had returned and Carson wasn't letting him go anytime soon. The Scotsman made certain Rodney or Ronon was with him at all times to prevent an escape. It was Rodney's turn to watch John and whenever he wasn't looking, he could feel Rodney's eyes on him. 

"What?" he finally growled.

"I was just thinking," was the quiet reply, completely unfazed by the tone his friend was using. "I mean, I knew there was some sort of connection between you and Elizabeth, but I didn't know it was so deep."

Rodney continued even though it seemed that John's face was getting paler by the minute. "I saw it in Antarctica. Once she saw you sitting in that chair she had to have you on the expedition, but it was more than that."

"Colonel Sheppard, are you all right?" Carson asked, rushing over. The man nodded, but looked a little worried about something. "Colonel?"

John blinked. "Rodney just made me realize something that I didn't want to face. Something I was afraid to admit because of what could happen. But I can't just turn off my feelings and I can't just hide from them."

Carson was slightly confused. "What are you on about, Colonel?"

"He's in love with Elizabeth as much as she's in love with him." John winced at Rodney's lack of subtlety. "What? Oh, like you were really going to admit it!"

"You could have given him the chance," Carson replied, as he checked John's blood pressure. "Just take a deep breath, Colonel. You'll be all right."

John nodded, but then looked up at Carson with eyes full of worry. "Have you been able to find something to counteract the drug she was given?"

"Not yet," he replied sadly.


	4. Chapter 4

Secrets of the Mind  
Part 4  
Disclaimers in part 1  
Notes: Again, thank you to the love xfirefly9x for being a wonderful beta reader! Also, thanks to those who have taken the time to review my fanfic. I really appreciate it! Please let me know what you think of this next part!

* * *

"If you look into your own heart, you find nothing wrong there, what is there to fear?" -Confucius

* * *

"Who is this?" Elizabeth asked.

Jack O'Neill shook his head. "I said don't touch anything."

"I-I just sat down," John replied nervously.

"Major, think about where we are in the solar system," Rodney suggested.

"Did I do that?" John asked as a map of the solar system appeared.

Elizabeth smiled, amazed by how strong the Ancient gene in this man was and the look of shock on his face was priceless. After about ten minutes, Rodney allowed him to get up.

She watched O'Neill and Daniel walk away, speaking in quiet tones, before she approached the soldier. "Major Sheppard, I'm Dr. Elizabeth Weir," she said.

"What the hell is going on around here?"

"Well," she replied, "My team and I are getting ready to embark on an expedition to another galaxy. The city we're going to has technology that would benefit from someone like you who has the gene. Are you interested in joining us?"

John just stared at her. She was amazed at the color of eyes and how he seemed to look right through her. She hated the quote, "love at first sight", but at that moment it seemed to apply. There was something about this man she couldn't place. She not only needed him for this mission, she wanted him.

"Major?"

"I'll think about it, Dr. Weir," he replied.

(The Rising Part 1)

* * *

"One more thing, Major -- something I'd like you to sleep on. I have a few thoughts on it myself but..."

"Thoughts about what?" John asked.

"Who the members of your team might be."

John was a little surprised to say the least. "My team?"

"Well," Elizabeth said, "you are the ranking military officer now, or do you need to be reminded of that? We need to get back out there; do what we came to do."

She leaned against the railing, looking out at the ocean as John walked over. "You do realize I can get us into all sorts of trouble, right?"

(The Rising Part II)

* * *

"This is Weir. What's the nature of Major Sheppard's injury?"

"Some sort of funky alien bug attached itself to his neck. He's completely immobile," Ford exclaimed.

Elizabeth's heart jumped into her throat. That was not something she wanted to hear. In fact, she wanted him safely within the walls of Atlantis. She had a good mind not to ever let him leave the city again.

45 minutes later and Elizabeth was rushing to the Jumper Bay. She sank to the bench as Carson said John was going to be okay. Now she had to worry about having a heart attack herself. She nearly lost him. Again!

Elizabeth joined John's team in the infirmary for a visit. "By the way, what were you going to say?"

"When?" he asked innocently.

"Before, when you thought, you know..."

"Oh, that."

She smiled. "I didn't want you to say it at the time, but now I'm curious."

"I was going to say, um…" John paused, "take care of each other."

"That's nice," Elizabeth replied, not totally convinced.

(38 Minutes)

* * *

"Have you ever tried to clear a stump by hand?" John asked.

Elizabeth was less than amused. "Yes, it's a hobby," she replied sarcastically.

(Underground)

* * *

Just as John beamed down from Deadelus, he said to the soldiers with him,"Secure Stargate Operations." He then looked around. "Well, I'm home."

John turned to see Elizabeth approaching. Suddenly she hugged him for several minutes then released him looking relieved. "Yes. You are. I truly thought ..."

"Yeah, yeah. I thought the same thing about you a minute ago. We gotta stop that."

Elizabeth chuckled. "I'd like that."

"So, uh, where are we?" John asked flustered.

(The Siege Part III)

* * *

"This is what I do when I have problems with my laptop, I turn it off and then I... turn it on again," John said.

Elizabeth shook her head, a small smile on her face. "I think this is a little bit more complicated than that."

"I'm just saying that if we're taking a page from the John Sheppard book of computer repair, we're really desperate."

(Intruder)

* * *

Elizabeth watched as memories flooded her mind. From her wonderful memories of Atlantis to the scariest, the Wraith, Genii. How they had survived she wasn't certain until that face appeared in her mind again.

John Sheppard.

He was an unbelievable soldier and an amazing friend. He was the one person they could count on in the messed up galaxy they were in. The one person Elizabeth could count on, the one person who didn't worry about opposing her, but also listened to her feelings.

Elizabeth's eyes snapped open and her heart was beating rapidly in her chest. She remembered everything. Including how she had promised herself not to tell John what she truly felt for him. They were definitely going to need to have a little chat.

"Elizabeth?" Teyla said, worry evident in her voice.

She blinked and smiled. "I'm all right. In fact, this has helped me so much, Teyla. True, I'm having a little difficulty remember what happened before coming to Atlantis and the last few days, but I think I've made much progress."

"That is wonderful," the Athosian replied. "I am certain everyone will be relieved to hear this. Especially Colonel Sheppard. I spoke with Rodney as you were meditating. He said that the Colonel had a set back and is in the infirmary again."

Elizabeth wanted to cry. It was her fault. She had run halfway through the city because her feelings had been irrationally skewed. "Is he all right?" she asked.

"I believe so. He was just a little winded and his fever has returned. I am sure he would like to see you, as would Carson."

"Okay," she said, swallowing around the lump in her throat. This is going to be awkward, she thought to herself.

* * *

"I have excellent news, Colonel," Carson said.

"You were able to create an antidote."

Carson nodded. "We were lucky. We accomplished it on our last sound theory. "

"Things are going to be really awkward between us if she remembers what happened after you give her that. Is there a possibility?"

"Of her forgetting? Aye. If she doesn't though, the two of you will have much to talk about, I suspect." John's only reply was a sarcastic chuckle. Carson didn't know what he could do to help his friends. How did one ignore the one person they felt a connection to?

Carson knew that if it were he in John's position, he'd act on it, the consequences be damned! He remembered a time when he was young. A time when he was compulsive and was determined to be the best physician on Earth.

And when sweet Heather had died, he regretted not taking a chance on loving her completely.

"Carson? You okay?"

"Aye, Colonel, I'm fine."

John didn't seem too convinced, but let it go for now. He was about to ask Carson when he could leave when Teyla entered the room… with Elizabeth. John took a deep breath and said, "Ladies."

"It is good to see you awake, John," Teyla said. "I trust you are feeling better?"

"Much. In fact, I was waiting for Carson to say the magic words."

Carson crossed his arms. "You are not leaving this infirmary until your temperature is back to normal, Son. Don't make me break out the large needles."

Teyla interrupted the two men. "Elizabeth has remembered her time on Atlantis, yet the memories of before she came and the most recent still elude her."

"Well," Carson said, "that's certainly good to hear. To add to that, we've come up with an antidote and as soon as you're ready I'll administer it."

Elizabeth nodded, her eyes focused on John and his on her. "Could you give us a few minutes, Carson?" she asked

"Of course. I have some things to get together. I'll be back soon." Carson looked at Teyla, who nodded and followed him.

"Hey," John said.

"Hey."

John cleared his throat. "This is… wow…"

Elizabeth nodded slowly, taking a seat. "I'm sorry."

"For what?"

"Kissing you."

"I'm not."

Elizabeth shook her head. "I'm serious, John. I shouldn't have done that, especially when I couldn't figure out what I was really feeling."

"I admit that at the time I was a little freaked out. I didn't want to admit that I had actually found someone. Not to mention the serious breach of protocol if we started seeing each other. I was afraid that if someone found out, one of us would be shipped out of here so fast our heads would spin. I don't want to leave here and I know you don't. I also know that if I was on Earth and something happened to you…"

"The feeling's mutual, John. I've come to realize that Atlantis itself wasn't the only reason I wanted to stay. It's because you're here!

"And, yes, I know I didn't show it when were on Earth after the Replicator fiasco, but I wanted time to think. I didn't know what to do."

John took her hand in his. "Maybe we should talk to someone on Earth about this. I love you too much to hide it anymore."

"I do too," Elizabeth said. Deep down she was worried about what that someone on Earth would say about their relationship, but she didn't say anything. Hopefully John wouldn't call her on it either. If Elizabeth had asked, she would know he was just as worried.

"Are you ready, Elizabeth?" Carson asked. Teyla was with him, Rodney and Ronon following.

Elizabeth nodded, placing a kiss on John's lips. The four in the immediate area already knew about them so there was no point in hiding it any longer. John smiled. "See you soon."

Ronon and Rodney exchanged a knowing grin as Carson led Elizabeth over to another bed to get situated. Teyla noticed the coloring on John's face. "Are you all right?" she asked with a small grin of her own.

"Okay, that's enough!" John exclaimed. "No more teasing your CO, that's an order!"

"But where's the fun in that?" Rodney asked.

Ronon nodded in agreement. "Besides, right now you're not on duty so technically you can't give us any orders."

John turned onto his side and closed his eyes. "Some people are trying to sleep around here!"

"Come," Teyla said. "We will leave him alone… For now."

John found himself chuckling at Teyla's dramatic pause as he drifted to sleep.


	5. Chapter 5

Secrets of the Mind

Part 5

Disclaimers in Part 1

From the Author: Again, thanks for the wonderful reviews. You guys really know how to boost an author's self esteem!

* * *

"You've got to be kidding me! You liked the books better than the movie?" 

Elizabeth looked over at John, raising an eyebrow. "And this surprises you?"

"I don't know. I guess. I still don't see how you prefer to read the Lord of the Rings trilogy rather than watch it. Tolkien is too wordy. I literally skipped through the Council of Elrond because I couldn't get through. I had a friend summarize it for me in about 10 minutes."

Elizabeth laughed. It was so good to have her memories back… all her memories. It was also wonderful to have a conversation with John after the huge mess she made of everything. Luckily they both felt the same way and it would all worked out (although they both still had some doubts about how the brass would take it all in).

"No wonder you haven't finished War and Peace," Elizabeth said with a grin.

John nodded in agreement. "I would like to finish it sometime this century, though."

Just then Rodney came in. He didn't make a sound as he slowly walked up to Elizabeth's bed. He looked absolutely worried, but he was amazingly silent.

"Rodney?" John asked, causing Elizabeth to turn and face the scientist. "What's wrong?"

Rodney didn't know how to tell them. He didn't know how to break the news to his friends that they were being called to Earth. He didn't know how to tell them that someone from Atlantis had sent an anonymous tip back to Earth with information regarding their new relationship.

"Rodney." Elizabeth took his hand and shook it.

He blinked. "Um, sorry. I just received a message from Earth. General Landry is requesting that you and Colonel Sheppard go as soon as Carson feels you're able."

"Feels they're able for what?" Carson asked, walking over.

"Gate travel apparently," John replied. "Did he say why?"

Rodney handed a piece of paper to Elizabeth. "That's why."

"Oh my God!"

"What?"

Elizabeth looked over at John. "Someone sent an anonymous message regarding our, and I quote, 'new found relationship'."

* * *

"Rodney relax, we'll be fine." 

He crossed his arms and eyed John skeptically. "That's what you keep saying, but from the way Colonel Caldwell was talking earlier, he didn't seem so convinced. And now I'm left alone with him while you're both on Earth."

"Don't worry so much, Rodney," Elizabeth said. "I'm sure we can smooth things over and be home by lunch."

John could tell that Rodney wasn't convinced, but he shrugged his shoulders and followed Elizabeth through the event horizon.

When they arrived, General Landry was waiting for them and he didn't look particularly happy. In fact, the man didn't even say anything, just gave them a look that said,_ Follow me now_! John didn't like silent orders like that all and from the expression on Elizabeth's face, he could tell she didn't either.

Elizabeth was taken to one of the guest quarters while John was taken to the briefing room. General O'Neill and Robert Woolsey were present. He greeted them then sat down after General Landry was seated.

"Colonel Sheppard," Landry began. "Do you know why you're here?"

John swallowed around the lump in his throat. "I think I have a good idea."

"Good, then this should be easy."

That's easy for you to say, John thought. Aloud he said, "Yes, Sir."

General Landry nodded to O'Neill. "Colonel, I realize that we've given you leeway on how things are run on Atlantis and I agree that it's been good for the city. The one thing we can't give in on is the policy of fraternization. This could split any focus either you or Dr. Weir have."

John nodded slowly, afraid to say anything. He had a sinking feeling he knew where this was going.

"Colonel," General Landry said, "If you both plan on continuing this relationship, you will have to be reassigned."

Woolsey could see the conflicting emotions in John's eyes. "You do understand why, Colonel?"

"Yes, Sir."

"We'll give you two hours to speak with Dr. Weir about this," O'Neill said. John couldn't be certain, but he thought he heard a hint of regret in his voice. "Of course we'd like both of you in Atlantis."

* * *

"Yes, Sir," John replied again, standing up. He gave a salute, then left to find Elizabeth. 

"Sir? What are you doing here?"

"Hey, Carter," Jack replied.

He purposely avoided the question. After what Carrie had said to him three years ago regarding resignation, he felt horrible that he couldn't provide the same reassurance to Sheppard. And he felt even worse that the man had to choose between the city he now called home and the woman he fell in love with.

Sam knew him almost as well as she knew herself. "What happened?"

"I can't discuss that with you, Sam," he replied. "Let's just say that I feel like I've just been zatted multiple times but without dying or disappearing."

"Sir… Jack."

He finally gave in.

* * *

Elizabeth stared at John for nearly five minutes before she spoke. "What are we going to do?" she asked. "They're probably going to order you to leave Atlantis whether or not we decide to pursue our relationship. 

"It's out now. Everyone is really going to believe that my… focus is split. I wish they knew me better than that. I care about everyone under my command equally! It doesn't matter if I'm in love with them or not, I don't plan on abandoning anyone!"

John quickly moved to take her into his arms as she cried. "I know all of that, Elizabeth," he said. "We're just going to have to prove that to General Landry and O'Neill. And the IOA."

"Haven't I proved it enough, John? I mean, apparently I've been harboring these feelings for awhile and they've never said anything about me splitting focus!"

John didn't know what to say to calm her down. He understood that if they wanted to be together, he had to stay. Even though Atlantis had become his home, he couldn't be so close to Elizabeth and not act on his feelings. At least if he were on Earth, she could visit him and they could be together.

"Elizabeth," he said, taking her hands in his. "I don't want to stay on Earth, but it looks like I may have to."

"John!"

He wrapped his arms tightly around her. "We'll work this through. You can visit me whenever you want. I will always be there for you. I love you."

Elizabeth allowed the tears to flow. "I love you too, John and I already miss you."

* * *

"It's Earth's IDC," Chuck told Rodney. 

He nodded. "Call Teyla and Ronon."

By the time he reached the bottom of the stairs, Elizabeth had walked through and the 'Gate shut down. Rodney felt his stomach drop to the floor. He had a pretty good idea what happened especially by the look on Elizabeth's face.

"Welcome home," he said.

"Yeah. Home."

"Elizabeth…"

"I'll be in my quarters, Rodney."

Rodney was half tempted to get some information from her. To find out what exactly had happened when they were on Earth. He was so lost in thought he didn't hear Ronon and Teyla come up behind him until Ronon's voice rumbled.

"Don't do that!" Rodney exclaimed, holding a hand to his chest. "Are you trying to give me a heart attack?"

Ronon just grinned as Teyla spoke up. "Where are Dr. Weir and Colonel Sheppard?"

"Elizabeth just went to her quarters."

"Sheppard?"

"He's not coming back."


	6. Chapter 6

Secrets of the Mind  
Part 6  
Disclaimers in Part 1  
Notes: Again thank you to xfirefly9x for being a wonderful beta. This is a little different with John and Elizabeth POVs.  
fyd818: That comment about John not being able read the Council of Elrond is all mine. I could not get my head around the part and had my friend summarize for me. Oh, and I'm a Sam/Jack Shipper too, LOL!  
cam-is-hot: Yes, indeed! Lets go stab the person who sent that message!!!

* * *

**JOHN **

I sighed and leaned back in the chair. The Daedalus would be bringing my belongings by when she returned. I sighed again when I realized I would be breaking in another team. I didn't seem to have luck working in the Milky Way Galaxy.

I remember yesterday before Elizabeth left. She took me to meet her Mother because she wanted us to have someone to go to. Jacqueline Weir had been authorized to know about the Stargate Program, but not exactly what was going on.

I smiled when the woman opened the door. I could definitely tell where Elizabeth received her beauty. "My sweet daughter, it is so good to see you!" Jacqueline exclaimed, hugging her tightly.

"It's good to see you too, Mom," she replied. "Something tells me you couldn't keep my visit a secret for very long."

Jacqueline laughed as she took in the cars in the driveway. "You know your brothers would have been angry with me if I didn't tell them you were coming for a visit."

"I know. Mom, I'd like you to meet John Sheppard."

"My but you're a handsome fellow," she said with a knowing grin. "Elizabeth Weir I can sense that this man is in love with you."

Elizabeth blushed. "Mom!"

I just shook my head with a smile. "I guess there's no point in hiding it, is there Mrs. Weir?"

"No point. But please, call me Jacqueline."

Jacqueline took me by the arm and led me into the living room. There I met Elizabeth's older brothers, Jason and Thomas Weir. I also met their wives and children. It was odd to see such a big family. I never had any siblings and neither did my parents.

Everyone was wonderful and very welcoming. I was happy that I could find some comfort from remaining on Earth even though deep down I wanted Elizabeth to stay so badly. I knew I couldn't do that to her. I knew that if I told her, she would stay regardless of Atlantis and what that city held.

I felt someone yanking on my hand and smiled at Elizabeth's four-year-old niece, Hannah. I knelt down and smiled at her. "Hi," she said shyly.

"Hi."

"Do you like Aunt 'Lizabeth?"

"I do."

She grinned. "Me too! She plays princess with me. Will you play princess with me?"

Jason laughed and walked over to us. "I'm sure John would love to play, but it's time for dinner."

"Yeah, Hannah," I said. "We'll play after dinner."

It's been a long time since I had a home cooked meal and Jacqueline Weir did not disappoint. I loved hearing stories of Elizabeth's childhood although I could tell she wasn't too keen on me hearing about her running naked through her Mom's garden when she was six.

After spending time with this wonderful family, I concluded that Jason took after Jacqueline and while Thomas and Elizabeth had many of their mother's qualities, must take after Jonathan Weir.

The most amazing thing is that I knew General Jonathan Weir. I had met him while I was stationed in Afghanistan. Before the whole black mark incident. He was the reason I hadn't been court martialed. I don't really know what he did to prevent that.

I guess I wouldn't be finding out any time soon. General Weir died the year before we left for the Pegasus Galaxy. Maybe one day I would find out, but right now I loved the fact that Elizabeth's dad liked me.

After dinner, Elizabeth's two nieces and her nephew surrounded me. Hannah and Rachel each decided they were princesses and I was the prince who was going to save them. Rachel's brother, Nathan said he was going to be the big dragon.

A kingdom saved and tragedy averted, it was late and the parents said it was time to go home. I gave them each a hug and told them we'll have plenty of time to have fun. "Bye John!" they exclaimed.

Thomas came over to shake my hand. "You're good for Elizabeth," he said. "Of course, if you hurt her, I'm sure you know what will happen."

"I do. She'll kick my ass."

Thomas laughed. "Exactly."

I was so lost in the memories that I almost didn't hear the knock at the door. "Sam," I greeted, standing up.

"Hey John. I was wondering if you'd like to join us for dinner tonight. Teal'c is in the mood for lasagna."

I really didn't want to eat lasagna with Teal'c, but I also didn't want to sit around and mope all day. I should probably lead somewhat of a normal life while I can. Besides, if Elizabeth knew I how I was acting, she wouldn't be happy with me.

"That'd be great," I told her. "Thanks."

* * *

**ELIZABETH**

I changed my mind about going to my quarters and finally arrived at my new destination: John's. I figured someone should start packing his things. I still couldn't believe what was happening. I couldn't believe that John was no longer in Atlantis.

I remembered introducing John to my family. I know he doesn't have anyone on Earth he to go to and I know that my family, Mom especially loves adopting others into our home.

I nearly cried at the sight of my Mom. The last time I saw her was in my mind while those damn nanites attacked my body.

"My sweet daughter, it is so good to see you!" Mom exclaimed, hugging me tightly.

"It's good to see you too, Mom," I replied. "Something tells me you couldn't keep my visit secret for very long."

Jacqueline laughed as she took in the cars in the driveway. "You know your brothers would have angry with me if I didn't tell them you were coming for a visit."

"I know. Mom, I'd like you to meet John Sheppard."

"My but you're a handsome fellow," she said with a knowing grin. "Elizabeth Weir I can sense that this man is in love with you."

I felt myself blush. "Mom!"

Amazingly, John just shook his head with a smile. "I guess there's no point in hiding it, is there Mrs. Weir?"

"No point. But please, call me Jacqueline."

I watched as Mom took John by the arm and escorted him into the living room to meet my brothers. I didn't want to leave John alone on Earth, so I needed to be certain there was someone who could be there for him.

"Hey little sis!" I suddenly hugged my older brother tightly and began to cry. "Elizabeth, are you all right?"

I nodded, but still held onto him. "Jason, this is going to be the hardest thing I've ever had to do." I went on to explain what I could to him. He was very understanding because we were used to living with classified military secrets.

"Don't worry, Elizabeth. We'll take care of John. I mean I know we just met him, but you know how much of a sixth sense Hannah has about new people. If there was something off about him, she would know."

"She would," I agreed. "Let me just run into the bathroom."

Jason smiled. "You look beautiful as always, sis."

"Looking beautiful and feeling beautiful are two different things, Jas," I told him as headed to the bathroom.

I learned something new about John today, my Dad too. Apparently they knew each other when they were stationed in Afghanistan. In fact, it was Dad who helped to save John's career. I remembered when Dad used to write to me about a young major by the name of John, but I never thought it could be him.

After dinner I laughed as I watched John play princesses and dragons with Hannah, Rachel, and Nathan. For someone who had no siblings, it was amazing to see how much of a natural he was with children.

I took a deep breath as I came back down to reality. I needed to get his belongings situated because the Daedalus would be leaving within the hour. As soon as that was taken care of, I went back up to my office. I needed to make an appearance or they would think something was wrong.

Who am I kidding? There is something wrong.

I sighed and sat down and realized that song was running through my mind. I remember hearing Lieutenat Cadman playing it one day and asking her who the singers were. The Dixie Chicks. I was never really into country, but now that I remember that song and it's lyrics, I feel as though they're my words...

Stepping out, everyone can see my face All the things I can't erase from my life Everybody knows

_Looking through the crowd  
I search for something else  
But every time I turn around  
I run into myself Here I stand  
Consumed with my surroundings  
Just another day Of everybody looking  
I swore they'd never see me cry_

But here I am, crying and when I look up at the noise I hear, I see Atlantis' flagship team with Carson Beckett standing before me.

* * *

The Dixie Chicks song is called "Everybody Knows" and I do not own it. 


	7. Chapter 7

Secrets of the Mind  
Part 7  
Disclaimers in Part 1  
Notes: Thanks again for the wonderful reviews and to my beta, xfirefly9x!

* * *

"Hey," she said quietly, no longer trying to hide the tears. "I'll be all right. Really."

Rodney sighed. "You don't seem very convinced yourself so I don't know how you plan on convincing us, Elizabeth. What exactly happened?"

She took a deep breath and stood up. "Basically they believe our relationship would split my focus."

Ronon grunted. "That's ridiculous."

"I agree, Elizabeth," Teyla said. "Your love for John has never hindered the success of this mission and the attempt to save everyone in this city and in this galaxy."

"There's nothing more we can do," Elizabeth replied in defeat. "It's done. John has been reassigned to the SGC."

"No!" Everyone looked at Carson. "I've never known you to give up so easily, Elizabeth. You know as much as I do that Colonel Sheppard belongs here! He is an asset to Atlantis. We need him here no matter what the IOA and military have to say!"

Rodney nodded in agreement. "I'm sure there are a great number of people who would rather have him here. I'm sure if we drafted a petition they would listen to us."

"Overly optimistic, aren't we, Rodney?" Elizabeth asked with a smile.

"Somebody has to be…"

And everyone knew the reason behind that comment. John was usually the optimistic one in the bunch and right now they needed him more than ever.

Rodney entered the mess hall to see a huge group of people gathered. Not only the military, but scientists as well. He glanced over at Elizabeth. "Are you sure you want people to know about this?"

Elizabeth nodded. "Yes, Rodney. I think they have a right to know. Besides, who's to say our little secret messenger didn't already begin gossiping?"

"True," he replied. Rodney then walked to center of the room and called for everyone's attention. "Most of you know that Colonel Sheppard's been reassigned. I don't know if the reason is known so we're going to talk a little about that and then we're going to talk about ways to get him back here."

Elizabeth took a seat next to Teyla. "Are you all right, Elizabeth?" she asked as Rodney continued to explain the situation.

"Yes, Teyla," she replied. "From what I see here, no one seems angry or upset about our relationship. They seem more eager to get John back here."

"I think Major Lorne is our top advocate on that," Ronon said with a smile.

Elizabeth smiled back. This had to work! Everyone on Atlantis was going to see to it. _Just hang on a little longer, John,_ she thought, _we'll bring you home._

* * *

John had finally been able to find a team he was comfortable with and vice versa. His team consisted of Dr. Angela Heinz, Major Henry Thyme, and Lieutenant Taylor Anderson. He still found it a little odd to visit a planet and not worry about an attack from the Wraith. As he walked around the decimated village, though, he remembered that Wraith could be killed.

The Ori on the other hand…

"Colonel Sheppard!"

"What is it, Lieutenant?" John asked.

"Tracks, Sir," Anderson replied. "Looks like some sort of animal. Big animal."

"Angela?"

The anthropologist walked over and knelt near Anderson to study the prints. "Whatever it is, Colonel, it's huge."

In response a long, malicious growl could be heard. "Okay, that's definitely not good and definitely close. Lets start back to the 'Gate," John suggested. "Major, take point. I've got our six."

"Yes, Sir!" Thyme said, P-90 at the ready.

John's eyes were trained as he followed his team, but his mind was elsewhere. His mind was in Atlantis along with his heart. It had only been three days but it felt like an eternity to him. Not only did he miss Elizabeth but all his friends and the city as well.

He was so lost in thought that he was too late to react and suddenly a creature as large as a lion pounced on him. John cried out as the creature slashed its claws through his TAC vest. It was about to take another swing when he heard a P-90 being fired.

The creature fell to the ground next to him with a thud. John just stared at in mild wonder as he attempted to catch his breath. His chest felt as if it were on fire and his breathing was getting worse.

"Colonel!" Angela exclaimed. "Major, dial Earth and send for a medical team!"

Major Thyme needed no further urging. Lieutenant Anderson kept an eye out for more of the creatures. "How the hell did we kill it?" he asked in confusion. "That thing was huge."

Angela ignored him as she gently opened John's vest. "Sorry, Colonel," she said when he groaned in pain. Her heart nearly stopped when she saw the extent of the damage and was grateful when Thyme told her the cavalry was on the way.

John felt the blood seeping through his chest and onto the ground. This was definitely not a good thing. All he wanted to do was sleep, but he knew if he did that, he would never wake up again.

Elizabeth. God, he wanted her with him so badly. He didn't want to die. There was so much he wanted to do with her. So much he wanted to say to her. She had changed his life in more ways than he ever could have imagined and now it was going to end.

"Elizabeth," he gasped out as Angela pressed gauze on the wound in an attempt to stop the flow of blood.

"Colonel?" Angela felt utterly helpless. John was dying right before her eyes and there wasn't a damn thing she could do about it.

"Here they come!" Thyme exclaimed in relief. He couldn't believe this was happening. This was only their second mission out as a team and already he was going to lose the newest member of his team.


	8. Chapter 8

Secrets of the Mind  
Part 8  
Disclaimers in Part 1  
Note from the author: I am so sorry for the delay in posting the final chapter of Secrets of the Mind. Again thank you all so much for your reviews and hope you enjoy the rest.

* * *

"Dr. Weir."

Elizabeth turned to see Major Lorne running up to her. "What can I do for you, Major?"

"Ma'am, even though we didn't actually state this in there, everyone is very happy for you and Colonel Sheppard. We all know that your loyalty isn't biased. I'll be including that in the petition."

"You're writing it?" she asked.

"I am," Lorne replied with a nod. "Teyla and I felt Dr. McKay, well…"

"He's not as adept with words as most people."

Lorne smiled. "I would never say that."

Before she could reply, they heard the alarms go off. "What's going on?" she asked, heading towards the control room.

"We have an incoming transmission from Earth," Chuck said.

Elizabeth's heart went into her throat. This was an unscheduled call and that was never a good thing. She nodded and spoke up. "Afternoon, General."

"Dr. Weir, I'm afraid I have some bad news."

Elizabeth took a deep breath._ 'Oh my God, he's dead!' _her mind screamed.

"Colonel Sheppard was attacked by some sort of creature while he was off world. Dr. Lam has given him sedatives to keep him calm, but he's agitated and won't sleep until he sees you."

"I'll be there as soon as possible, General. Thank you. Weir out."

Once the 'Gate shut down there was total silence in the control room. That is, until Rodney came in complaining about something or another. He stared at Elizabeth. Her face was pale and she seemed to be trembling.

Rodney rushed to her side. "What's wrong?"

"John."

"What? What about him?" Rodney realized something must have happened to his friend because everyone in the room was just sitting around and Elizabeth looked ready to crumble into a heap on the floor. His eyes widened. "Is he…?"

"No, Rodney," Elizabeth said when she found her voice. "He's alive, but I have to go to Earth. He needs me."

He nodded. "Would you like one of us to come with you?"

"Not right now, Rodney," she replied. "I'll send a message through as soon as I can, though."

* * *

Elizabeth entered the infirmary with caution. She wanted to see John but she didn't know if she was prepared. From what General Landry told her, he had been attacked by a lion-like creature and slashed across the chest. He had lost a lot of blood by the time Dr. Lam and her team arrived.

"Dr. Weir."

"Hello, Dr. Lam," she said quietly. "How is he?"

"Still highly agitated. I can tell he's exhausted, but we just can't get him to sleep. I've put him on as much sedative as I'm comfortable with, but he's fighting. I'm hoping that once he sees you're here, he'll get some rest."

Elizabeth nodded as she followed Dr. Lam. She was directed towards the back of the infirmary behind a curtained off area. Elizabeth felt sick to her stomach when she heard his weak voice asking for her. She swallowed around the lump in her throat and stepped towards him.

John didn't want to fall asleep. Not until Elizabeth arrived. He was told she was called about an hour ago, but she still wasn't there. He hated acting like a baby, but if he was going to close his eyes, he wanted to see her just in case he never woke up again.

"John."

"Thanks for coming," he said weakly. "I just really wanted to see you."

Elizabeth smiled. "You couldn't have requested my presence in an easier way?"

John laughed, but immediately regretted it as spikes of pain flowed like running water.

She kissed him softly on the lips. "Why don't you try to get some sleep? I'll be here when you wake, I promise."

"Okay," he said. "Love you."

"I love you too, John," she replied with a smile.

Elizabeth made certain he was asleep before heading to Dr. Lam's office. "Dr. Weir, come in," she said when Elizabeth knocked.

"He's finally asleep."

"Good," Dr. Lam replied. "I was worried. He's lost a significant amount of blood and he needs all the rest he can get to regain his strength. I was wondering how Dr. Beckett doesn't have gray hair dealing with Colonel Sheppard."

Elizabeth smiled. "You might want to ask him because I have no idea. I know I keep mine hidden with hair dye."

* * *

John woke up in some pain, but felt more awake than he had and very happy to see Elizabeth lying on a bed across from him. He didn't want to wake her yet. He just wanted to watch her sleeping peacefully. He never thought he'd find anyone as smart or beautiful as Elizabeth and that someone like her would actually return feelings for him.

John knew that despite the fact that they were stuck galaxies apart he would continue to love and care for her the rest of his life.

"Excuse me Colonel Sheppard," a voice said.

John turned to see General Landry. "Sir."

"How are you feeling?"

"Much better, Sir, thank you." John looked at his hands. "And thank you for," he cleared his throat, "for allowing Elizabeth to come here."

Landry waved his hand in dismissal of the thanks. "I remember when my wife used to look at me the way Dr. Weir looks at you." The General paused a moment. "Colonel, Woolsey would like to meet with you to further discuss your position with the Stargate Program."

"That doesn't sound very fun…"

"Believe me, you'll want to be there!" Landry replied.

* * *

John blinked as he glanced over at Elizabeth. He had a feeling that the look of shock on her face mirrored his own. "Not that I'm one to look a gift horse in the mouth," he said, "but what made you change your minds?"

"This," Woolsey replied, handing John a file.

John opened it with curious eyes. He moved closer to Elizabeth so she could read it as well. It was a petition signed by every scientist and military personnel in Atlantis.

John Sheppard was absolutely speechless. True, he knew that he had gained respect by most everyone there, but he didn't dare to hope that any of them would go so far as to have him return especially with the fact that he and Elizabeth were together.

"Colonel, the IOA is willing to give this a try. From what I've read in that petition, the people there trust you both so I believe we can as well," Woolsey said. "So, are you ready to go back to Atlantis?"

John smiled as he looked at Elizabeth. "I'm ready to go home."

* * *

"Wait a minute!" Jacqueline called out. John and Elizabeth turned to see her coming up to them, a covered dish in her hands. "John, you need to keep your strength up while you're recuperating so I put some of that pot roast in here for you."

John grinned, accepting the dish. "Thanks, Jacqueline. I really appreciate everything you've done for me."

"No need to thank me, dear," she replied. "Just keep my daughter happy and we'll be even."

"I plan to," John replied.

Jacqueline smiled as she gave him and Elizabeth another hug. "Now I don't want either of you to work yourselves too hard! I expect you to be home for either Thanksgiving or Christmas, is that understood?"

The pair laughed and said, "Yes, Ma'am!"

* * *

Carson glanced over at Teyla as they entered the mess hall. Rodney was standing on a chair adjusting the banner that stated, _"Welcome Home, John!"_

Ronon just shook his head. "You're gonna fall, McKay."

"I'll be fine," Rodney replied annoyed. "I don't see you offering to help me."

Before Ronon could reply, the ladder suddenly teetered and Rodney was falling to the floor. To Carson it seemed to happen in slow motion as he saw Ronon rush over and deftly catch Rodney in his arms. He had to stifle a laugh at the look on their faces when they realized what they must look like.

"Rodney," Teyla said, attempting to hold in her laughter. "Are you all right?"

Rodney glared at them as Ronon set him onto the floor. "I do not want to hear it! That was so not funny!"

"Of course not, Rodney," Carson said.

* * *

John and Elizabeth were waiting as the 'Gate dialed when his former team arrived to say their good-byes. "It was fun while it lasted," he told them. "Although I could have done without the animal attack."

"Same here, Sir," Anderson replied.

Angela nodded in agreement. "I think my stomach was in my throat all week after that!"

"I hope you'll keep in touch, Sir," Thyme said.

"I will," John told him as the 'Gate sprang to life. He looked over at Elizabeth, taking her hand. "Ready?"

She nodded. "As I'll ever be."

All was quiet in Atlantis upon arrival. John didn't really think anything of it. "I should probably check in with Carson."

"Good idea," Elizabeth replied. "How about you meet me in the mess hall? I'll get Rodney, Teyla, and Ronon as well."

"Great idea."

John wasn't sure if he should kiss her, but Elizabeth made the decision for them and soon he was standing in the middle of the Gateroom blushing like a schoolboy. With a shake of his head and a grin, John headed to the infirmary.

"Colonel," Carson said. "Welcome back."

John smiled, shaking his hand. "It's good to be back, Doc."

"I just finished reading Dr. Lam's report. I see your stubbornness is not exclusive to the Pegasus Galaxy." John only shrugged as he climbed onto one of the beds so could Carson could check his bandages. "Elizabeth tells me you met her family."

"Yeah," John replied grinning. "They're fantastic, especially her nieces and nephew. Although I found out her Dad, General Jonathan Weir was the reason for me not being discharged."

"That's amazing. What are the chances of that?"

"Pretty slim."

John went on to explain that he served under General Weir and even though the man disapproved of John going back against his order, the General realized why and that he would have done the same. Elizabeth also told him that he would write her letters about a certain Air Force major.

Carson wasn't surprised that John endeared himself to such a man. It was also nice to know that he was treated with the respect he deserved.

"Well, Colonel, you're free to go."

"Thanks, Doc," John said. "Would you like join me in the mess hall?"

* * *

"They're heading over!" Rodney said. He smiled. This was going to be great and having his best friend back was definitely a plus.

The look of shock on John's face when he entered the mess hall was priceless. He didn't even expect anything. Glancing at Lorne, he shook his head and walked over to him.

"And who said we could have a party?"

Lorne shrugged. "Oh, you know those civilians, Sir. Any excuse to have one. Welcome home."

"Thanks," John replied, shaking his hand. He turned to face everyone there. "Thanks to all of you! I have to admit I don't know what I've done to deserve all of this, but I have never felt more grateful than I do right now."

"You deserve all of this, Colonel," Lorne told him. "Many of us would be dead right now if it hadn't been for you..."

"Hey!"

Lorne chuckled. "Or you, Dr. McKay."

Elizabeth walked over to him, taking his hand in hers. "John, everyone here considers you part of our family. The past week and half was hard on us and we are so happy to have you back."

John grinned. "I'm happy to be back."

And somehow, towards the end of the party, John Sheppard had a Polaroid handed to him. He laughed. Blackmail was such an evil thing, but looking at the picture of Rodney in Ronon's arms, it was too great an opportunity to pass up.


End file.
